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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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The SGE Option #1

Closed chenshixuan closed 5 years ago

chenshixuan commented 5 years ago

Hi,hujiang: The SGE parameter is not so fit to my SGE system .On my SGE, We must echo the Project name ,vf,and cpu number,the job will be submitted.I found that ,your mode is like falcon,so could you add some parameters like falcon? job_queue = all.q sge_option_da = -P 1234 -l vf=18G -q %(job_queue)s -l num_proc=4
sge_option_la = -P 1234 l vf=30G -q %(job_queue)s -l num_proc=4
Thank you !

moold commented 5 years ago

Thank you for your suggestion, I will fix this as soon as possible.

moold commented 5 years ago

Hi, I have fix this. Please update NextDenovo and use sge_options = -P 1234 -l vf={vf} -q all.q -l num_proc={cpu} in your config file. Please do not change {vf} and {cpu}, NextDenovo will automatically replace to the required resources for different steps.